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A behavioral lifestyle intervention with partial meal replacement reduced excess gestational weight gain in ethnically diverse women with overweight/obesity, but the effects on micronutrient intake remained unknown. A secondary analysis of a randomized, controlled trial tested whether the intervention improved micronutrient intake relative to usual care. Pregnant women (<i>n</i> = 211; 30.5 years of age, body mass index, BMI, of 32.0 kg/m²) were enrolled and randomized within site and ethnicity (40% were Hispanic) into intervention (<i>n</i> = 102) or usual care (<i>n</i> = 109) groups. Two 24 h dietary recalls were conducted on random days at study entry and late pregnancy (35–36 weeks gestation). Nutrient adequacy was defined using the Estimated Average Requirement cut-point method. At study entry and including prenatal vitamins, ≥90% of participants reported inadequate intake of vitamins D and E and iron; 40–50% reported inadequate intake of calcium, protein, vitamins A, C, B₆, folate, magnesium, and zinc. From study entry to late pregnancy, the behavioral intervention with partial meal replacement increased the overall intake of vitamins A, E, and D and copper and reduced the odds of inadequate intake of calcium (odds ratio (OR) = 0.37 (0.18, 0.76)), vitamins A (OR = 0.39 (0.21, 0.72)) and E (OR = 0.17 (0.06, 0.48)), and magnesium (OR = 0.36 (0.20, 0.65)). A behavioral intervention with partial meal replacement during pregnancy improved the intake of several micronutrients in Hispanic and non-Hispanic women with overweight/obesity.